AutoCloner

Multiple sequence alignment - TraesCS1B01G398600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G398600	chr1B	100.000	3333	0	0	1	3333	629701739	629705071	0.000000e+00	6156.0
1	TraesCS1B01G398600	chr1B	94.481	3352	128	24	1	3333	6339701	6343014	0.000000e+00	5112.0
2	TraesCS1B01G398600	chr1B	96.188	2492	66	10	1	2486	6694207	6691739	0.000000e+00	4048.0
3	TraesCS1B01G398600	chr1B	93.282	774	49	2	1	774	6530757	6529987	0.000000e+00	1138.0
4	TraesCS1B01G398600	chr1B	82.296	1141	165	29	906	2028	7130214	7129093	0.000000e+00	953.0
5	TraesCS1B01G398600	chr1B	82.049	1142	169	25	905	2028	7928368	7927245	0.000000e+00	941.0
6	TraesCS1B01G398600	chr1B	81.699	1142	167	26	905	2028	6326385	6327502	0.000000e+00	913.0
7	TraesCS1B01G398600	chr1B	97.175	531	11	3	769	1297	6523803	6523275	0.000000e+00	894.0
8	TraesCS1B01G398600	chr1B	85.514	428	36	11	2859	3279	5737949	5738357	1.110000e-114	424.0
9	TraesCS1B01G398600	chr1B	87.500	376	34	9	2466	2830	6691724	6691351	3.980000e-114	422.0
10	TraesCS1B01G398600	chr1D	80.000	1655	218	54	901	2542	3227924	3229478	0.000000e+00	1118.0
11	TraesCS1B01G398600	chr1D	79.686	1147	186	31	906	2028	3122989	3124112	0.000000e+00	784.0
12	TraesCS1B01G398600	chr1D	82.250	800	110	23	905	1682	3614497	3615286	0.000000e+00	662.0
13	TraesCS1B01G398600	chr1D	81.293	433	64	7	2090	2508	3615610	3616039	5.330000e-88	335.0
14	TraesCS1B01G398600	chr1D	84.536	291	38	5	1730	2018	3615295	3615580	7.040000e-72	281.0
15	TraesCS1B01G398600	chr1A	82.091	899	138	16	1100	1991	6499048	6498166	0.000000e+00	747.0
16	TraesCS1B01G398600	chr1A	85.335	641	79	11	897	1536	6439204	6438578	0.000000e+00	649.0
17	TraesCS1B01G398600	chr1A	87.113	194	22	3	901	1092	6500196	6500004	2.010000e-52	217.0
18	TraesCS1B01G398600	chrUn	81.295	556	83	11	905	1443	9820636	9820085	6.610000e-117	431.0
19	TraesCS1B01G398600	chrUn	86.581	313	38	1	1392	1704	9820066	9819758	3.180000e-90	342.0
20	TraesCS1B01G398600	chrUn	82.645	363	53	8	2090	2448	9819459	9819103	2.500000e-81	313.0
21	TraesCS1B01G398600	chrUn	84.727	275	36	5	1744	2018	9819757	9819489	1.520000e-68	270.0
22	TraesCS1B01G398600	chr7A	81.944	72	11	2	3043	3112	612701890	612701961	3.590000e-05	60.2
23	TraesCS1B01G398600	chr6D	92.683	41	2	1	2810	2849	58061820	58061860	1.290000e-04	58.4

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G398600	chr1B	629701739	629705071	3332	False	6156	6156	100.000	1	3333	1	chr1B.!!$F4	3332
1	TraesCS1B01G398600	chr1B	6339701	6343014	3313	False	5112	5112	94.481	1	3333	1	chr1B.!!$F3	3332
2	TraesCS1B01G398600	chr1B	6691351	6694207	2856	True	2235	4048	91.844	1	2830	2	chr1B.!!$R5	2829
3	TraesCS1B01G398600	chr1B	6529987	6530757	770	True	1138	1138	93.282	1	774	1	chr1B.!!$R2	773
4	TraesCS1B01G398600	chr1B	7129093	7130214	1121	True	953	953	82.296	906	2028	1	chr1B.!!$R3	1122
5	TraesCS1B01G398600	chr1B	7927245	7928368	1123	True	941	941	82.049	905	2028	1	chr1B.!!$R4	1123
6	TraesCS1B01G398600	chr1B	6326385	6327502	1117	False	913	913	81.699	905	2028	1	chr1B.!!$F2	1123
7	TraesCS1B01G398600	chr1B	6523275	6523803	528	True	894	894	97.175	769	1297	1	chr1B.!!$R1	528
8	TraesCS1B01G398600	chr1D	3227924	3229478	1554	False	1118	1118	80.000	901	2542	1	chr1D.!!$F2	1641
9	TraesCS1B01G398600	chr1D	3122989	3124112	1123	False	784	784	79.686	906	2028	1	chr1D.!!$F1	1122
10	TraesCS1B01G398600	chr1D	3614497	3616039	1542	False	426	662	82.693	905	2508	3	chr1D.!!$F3	1603
11	TraesCS1B01G398600	chr1A	6438578	6439204	626	True	649	649	85.335	897	1536	1	chr1A.!!$R1	639
12	TraesCS1B01G398600	chr1A	6498166	6500196	2030	True	482	747	84.602	901	1991	2	chr1A.!!$R2	1090
13	TraesCS1B01G398600	chrUn	9819103	9820636	1533	True	339	431	83.812	905	2448	4	chrUn.!!$R1	1543

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
355	357	0.032130	TGCAGGTTCACGAGTGTCTC	59.968	55.0	2.97	0.0	0.0	3.36	F
2194	3263	0.250467	ACTTTGGTCAGCAGCGTCAT	60.250	50.0	0.00	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2235	3304	0.543277	CTATCTGGAACCTGGCTGCA	59.457	55.000	0.5	0.0	0.0	4.41	R
3113	4247	1.067635	GCGGGCACAACATTTGATCTT	60.068	47.619	0.0	0.0	0.0	2.40	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	2.656560	AGTTCGTGTACTCCATGCTC	57.343	50.000	0.00	0.00	0.00	4.26
210	212	2.596452	CACTTATATACGGCAGCCTCG	58.404	52.381	10.54	0.00	0.00	4.63
216	218	1.802337	ATACGGCAGCCTCGCGAATA	61.802	55.000	11.33	0.00	0.00	1.75
320	322	0.457509	CGTTCACTGCTCAGAGCGAT	60.458	55.000	17.81	5.14	46.26	4.58
355	357	0.032130	TGCAGGTTCACGAGTGTCTC	59.968	55.000	2.97	0.00	0.00	3.36
356	358	0.315568	GCAGGTTCACGAGTGTCTCT	59.684	55.000	2.97	0.00	0.00	3.10
364	366	4.498894	TCACGAGTGTCTCTATCCCTTA	57.501	45.455	2.97	0.00	0.00	2.69
699	701	1.811359	CAAGAGGAAGACGACGGTAGT	59.189	52.381	0.00	0.00	0.00	2.73
707	709	2.075338	AGACGACGGTAGTCTCAGTTC	58.925	52.381	16.75	0.00	44.87	3.01
752	754	4.595781	AGGTCACGGGCCATTCTTTATATA	59.404	41.667	4.39	0.00	0.00	0.86
753	755	5.250774	AGGTCACGGGCCATTCTTTATATAT	59.749	40.000	4.39	0.00	0.00	0.86
810	812	7.147742	CCCACCTGCCACATAACTTTTATATTT	60.148	37.037	0.00	0.00	0.00	1.40
900	904	5.007823	CGTGACAAAACCACCAACTACATAA	59.992	40.000	0.00	0.00	0.00	1.90
1540	2589	7.855904	GTCGCCAAAGTAATCCAAAATATACAG	59.144	37.037	0.00	0.00	0.00	2.74
1601	2650	0.250858	CTGTCTGTGCATCCCCAACA	60.251	55.000	0.00	0.00	0.00	3.33
1700	2752	9.436957	CTCACTTAGTAACTTGGATTTACACAT	57.563	33.333	0.00	0.00	32.70	3.21
1832	2891	1.140052	TGCCTCGTTCTCTTCAAACCA	59.860	47.619	0.00	0.00	0.00	3.67
1849	2908	3.071874	ACCATGACAATTCGATGTGGT	57.928	42.857	0.00	0.00	32.57	4.16
2117	3186	2.005451	CTTGCTCCTTCCGAGTTCATG	58.995	52.381	0.00	0.00	41.10	3.07
2194	3263	0.250467	ACTTTGGTCAGCAGCGTCAT	60.250	50.000	0.00	0.00	0.00	3.06
2266	3335	6.480320	CAGGTTCCAGATAGTAACACTATTGC	59.520	42.308	0.63	0.00	41.21	3.56
2340	3409	1.255882	TGCCCAATTTAGCACAGTGG	58.744	50.000	1.84	0.00	33.08	4.00
2387	3456	2.041686	GGCTCTGGTCGACGACTCT	61.042	63.158	25.87	0.00	32.47	3.24
2393	3462	2.233186	TCTGGTCGACGACTCTCTTCTA	59.767	50.000	25.87	2.73	32.47	2.10
2436	3517	3.233355	AGGATTGTCCTTGTCGTGC	57.767	52.632	0.00	0.00	46.91	5.34
2649	3774	6.997942	AAGGACAAGTTTAGGTCTCTAACT	57.002	37.500	0.00	0.00	35.40	2.24
2652	3777	5.480205	GACAAGTTTAGGTCTCTAACTGGG	58.520	45.833	0.00	0.00	35.40	4.45
2656	3781	4.020128	AGTTTAGGTCTCTAACTGGGCAAG	60.020	45.833	0.00	0.00	35.40	4.01
2683	3809	3.793559	GTAGCATACAATTCGAGGTGGT	58.206	45.455	2.89	0.00	42.43	4.16
2698	3824	1.674817	GGTGGTAAGGACGTGGTCATG	60.675	57.143	0.00	0.00	33.68	3.07
2709	3835	4.188462	GACGTGGTCATGAATGTGGATAA	58.812	43.478	0.00	0.00	32.09	1.75
2717	3843	8.902806	TGGTCATGAATGTGGATAAAATTCTAC	58.097	33.333	0.00	0.00	32.63	2.59
2763	3889	1.745087	TCGAATCATCCTTTGGCAAGC	59.255	47.619	0.00	0.00	0.00	4.01
2804	3931	2.398498	CTGAGAAACTGTCGGACACTG	58.602	52.381	6.76	1.03	0.00	3.66
2823	3950	3.007614	ACTGCTGAAATTACACCCTACGT	59.992	43.478	0.00	0.00	0.00	3.57
2831	3958	1.308069	TACACCCTACGTCGAGTGCC	61.308	60.000	1.50	0.00	33.46	5.01
2885	4012	4.341487	AGGCGCCCTTTTACTTCTTTATT	58.659	39.130	26.15	0.00	0.00	1.40
2911	4042	7.048512	AGTTACTTATTATTCTGGGTGCACTC	58.951	38.462	17.98	14.58	0.00	3.51
2935	4066	5.391843	CCAATGTTTGACGATGCAGTTATGA	60.392	40.000	0.00	0.00	0.00	2.15
2988	4119	8.991243	TCTACGCTACTATTAAAAGAGCAAAA	57.009	30.769	0.00	0.00	32.55	2.44
3048	4180	7.045416	TCTCTTAAAGCAACACAGTAAACTGA	58.955	34.615	16.74	0.00	46.59	3.41
3052	4184	5.835113	AAGCAACACAGTAAACTGAACAT	57.165	34.783	16.74	0.00	46.59	2.71
3062	4194	9.639601	CACAGTAAACTGAACATGAGATAACTA	57.360	33.333	16.74	0.00	46.59	2.24
3065	4197	9.256228	AGTAAACTGAACATGAGATAACTAGGA	57.744	33.333	0.00	0.00	0.00	2.94
3113	4247	4.019792	TCCTACCGCCATATTACGTCTA	57.980	45.455	0.00	0.00	0.00	2.59
3129	4263	5.283060	ACGTCTAAGATCAAATGTTGTGC	57.717	39.130	0.00	0.00	0.00	4.57
3135	4270	0.896923	ATCAAATGTTGTGCCCGCAT	59.103	45.000	0.00	0.00	0.00	4.73
3163	4298	3.192230	CCGCCAGCGTTCGCATAA	61.192	61.111	18.95	0.00	37.81	1.90
3171	4306	2.284952	CAGCGTTCGCATAATGTGATCA	59.715	45.455	18.95	0.00	36.69	2.92
3181	4316	2.779755	AATGTGATCACTACGGGCAA	57.220	45.000	25.55	4.07	0.00	4.52
3184	4319	0.108138	GTGATCACTACGGGCAAGCT	60.108	55.000	18.83	0.00	0.00	3.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	4.559251	GTCAGCAAACTCAGATGTAGTACG	59.441	45.833	0.00	0.00	0.00	3.67
210	212	6.035843	TGGAAAGCTTGATTCATTTATTCGC	58.964	36.000	0.00	0.00	0.00	4.70
320	322	2.419990	CCTGCAAATCACCTGTCCGATA	60.420	50.000	0.00	0.00	0.00	2.92
364	366	3.380637	GCTGCTGATTGACTTGAATCCAT	59.619	43.478	0.00	0.00	32.20	3.41
699	701	1.827399	GCTCCCCAACGGAACTGAGA	61.827	60.000	0.00	0.00	41.40	3.27
752	754	6.772716	CACATAAATTAGTTGGGGCTCACTAT	59.227	38.462	0.00	0.00	0.00	2.12
753	755	6.119536	CACATAAATTAGTTGGGGCTCACTA	58.880	40.000	0.00	0.00	0.00	2.74
1540	2589	3.909285	GTACGCCCGGGAGTAGGC	61.909	72.222	34.27	21.19	46.17	3.93
1724	2781	1.089920	GCAGGTGATCAAGCGTCATT	58.910	50.000	0.00	0.00	0.00	2.57
1728	2785	2.045926	GGGCAGGTGATCAAGCGT	60.046	61.111	0.00	0.00	0.00	5.07
1768	2827	4.785453	CCGTCTGCTCCCCAAGGC	62.785	72.222	0.00	0.00	0.00	4.35
1832	2891	2.672874	CGTCACCACATCGAATTGTCAT	59.327	45.455	0.00	0.00	0.00	3.06
1849	2908	4.647611	ACCCAATTGAGTTAATCACGTCA	58.352	39.130	7.12	0.00	37.77	4.35
2068	3137	1.066914	CAAGAGAAGAGTGCGTCAGC	58.933	55.000	0.00	0.00	45.41	4.26
2069	3138	1.066914	GCAAGAGAAGAGTGCGTCAG	58.933	55.000	0.00	0.00	0.00	3.51
2117	3186	4.096382	TCAGTTGTTCCAAGAACTTGCTTC	59.904	41.667	8.81	2.76	40.12	3.86
2149	3218	4.449068	GTGATGTAACAACAGTCACTCCTG	59.551	45.833	10.87	0.00	36.98	3.86
2194	3263	3.464720	TTCCAAAAGGCCCATATGTCA	57.535	42.857	0.00	0.00	0.00	3.58
2235	3304	0.543277	CTATCTGGAACCTGGCTGCA	59.457	55.000	0.50	0.00	0.00	4.41
2266	3335	3.261951	CACGCGCATAGAACCCCG	61.262	66.667	5.73	0.00	0.00	5.73
2290	3359	1.818674	CCAAGTGCATTAACAGACCCC	59.181	52.381	0.00	0.00	0.00	4.95
2291	3360	2.749621	CTCCAAGTGCATTAACAGACCC	59.250	50.000	0.00	0.00	0.00	4.46
2387	3456	9.177608	CATTGTTGGAATACTGGAAATAGAAGA	57.822	33.333	0.00	0.00	0.00	2.87
2628	3751	5.480205	CCAGTTAGAGACCTAAACTTGTCC	58.520	45.833	0.00	0.00	36.69	4.02
2631	3756	4.254492	GCCCAGTTAGAGACCTAAACTTG	58.746	47.826	0.00	0.00	36.69	3.16
2649	3774	0.692476	ATGCTACAGTGTCTTGCCCA	59.308	50.000	0.00	0.00	0.00	5.36
2652	3777	5.551760	AATTGTATGCTACAGTGTCTTGC	57.448	39.130	0.00	3.88	40.24	4.01
2656	3781	4.504461	CCTCGAATTGTATGCTACAGTGTC	59.496	45.833	0.00	0.00	40.24	3.67
2680	3806	1.634960	TCATGACCACGTCCTTACCA	58.365	50.000	0.00	0.00	0.00	3.25
2683	3809	3.595173	CACATTCATGACCACGTCCTTA	58.405	45.455	0.00	0.00	0.00	2.69
2698	3824	6.912591	CGGCAAGTAGAATTTTATCCACATTC	59.087	38.462	0.00	0.00	0.00	2.67
2709	3835	1.064685	CCTCCCCGGCAAGTAGAATTT	60.065	52.381	0.00	0.00	0.00	1.82
2763	3889	3.506067	AGCAAGTTAAAGGTTCAATCCCG	59.494	43.478	0.00	0.00	0.00	5.14
2804	3931	2.601763	CGACGTAGGGTGTAATTTCAGC	59.398	50.000	5.77	5.77	35.43	4.26
2831	3958	2.678336	GGTCCTTTGCCGAGTATTTCTG	59.322	50.000	0.00	0.00	0.00	3.02
2885	4012	8.086143	AGTGCACCCAGAATAATAAGTAACTA	57.914	34.615	14.63	0.00	0.00	2.24
2904	4035	1.601903	TCGTCAAACATTGGAGTGCAC	59.398	47.619	9.40	9.40	0.00	4.57
2911	4042	2.995466	ACTGCATCGTCAAACATTGG	57.005	45.000	0.00	0.00	0.00	3.16
2982	4113	5.335661	CGGGTTAGCAGAGTTTATTTTTGCT	60.336	40.000	2.68	2.68	46.03	3.91
2988	4119	3.343941	TGCGGGTTAGCAGAGTTTATT	57.656	42.857	0.00	0.00	42.92	1.40
3026	4158	7.247728	TGTTCAGTTTACTGTGTTGCTTTAAG	58.752	34.615	9.53	0.00	44.12	1.85
3027	4159	7.147143	TGTTCAGTTTACTGTGTTGCTTTAA	57.853	32.000	9.53	0.00	44.12	1.52
3034	4166	8.774586	GTTATCTCATGTTCAGTTTACTGTGTT	58.225	33.333	9.53	0.00	44.12	3.32
3048	4180	7.496346	TCAAAGGTCCTAGTTATCTCATGTT	57.504	36.000	0.00	0.00	0.00	2.71
3113	4247	1.067635	GCGGGCACAACATTTGATCTT	60.068	47.619	0.00	0.00	0.00	2.40
3147	4282	1.368019	CATTATGCGAACGCTGGCG	60.368	57.895	19.32	13.56	46.03	5.69
3154	4289	4.085055	CCGTAGTGATCACATTATGCGAAC	60.085	45.833	27.02	9.58	0.00	3.95
3160	4295	4.380531	CTTGCCCGTAGTGATCACATTAT	58.619	43.478	27.02	9.48	0.00	1.28
3163	4298	1.743772	GCTTGCCCGTAGTGATCACAT	60.744	52.381	27.02	14.51	0.00	3.21
3171	4306	3.234630	TTGCGAGCTTGCCCGTAGT	62.235	57.895	23.34	0.00	0.00	2.73
3181	4316	3.612247	AATCAGGGCGTTGCGAGCT	62.612	57.895	0.00	0.00	34.52	4.09
3184	4319	1.599518	ACAAATCAGGGCGTTGCGA	60.600	52.632	0.00	0.00	0.00	5.10
3191	4326	1.303309	CTCGATCCACAAATCAGGGC	58.697	55.000	0.00	0.00	0.00	5.19
3290	4425	8.400947	CAGTGACCATATTGTATTTCTCCAAAG	58.599	37.037	0.00	0.00	0.00	2.77
3293	4428	6.069673	ACCAGTGACCATATTGTATTTCTCCA	60.070	38.462	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.